nf_modules: update alntools awk

src/nf_modules/alntools/main.nf

@@ -21,14 +21,14 @@ process bam2ec {
 
   script:
 """
-awk -F"[\\t;]" '
+awk -F"[\t;]" '
 \$3=="exon" {
         ID=gensub(/transcript_id \"(.*)\"/, "\\1", "g", \$11); 
         LEN[ID]+=\$5-\$4+1;
     } 
 END{
     for(i in LEN)
-        {print i"\\t"LEN[i]}
+        {print i"\t"LEN[i]}
     }
 ' ${gtf} > ${gtf.simpleName}_transcripts_lengths.tsv
 alntools bam2ec ${params.bam2ec} -t ${gtf.simpleName}_transcripts_lengths.tsv -c 8 ${bam} ${bam.simpleName}.bin

src/nf_modules/kb/main.nf

@@ -102,7 +102,7 @@ workflow count {
   switch(params.kb_protocol) {
     case "marsseq":
       split(fastq, config)
-      kb_marseq(index, split.out.fastq.view(), transcript_to_gene, whitelist_optional)
+      kb_marseq(index.collect(), split.out.fastq.view(), transcript_to_gene, whitelist_optional)
       kb_marseq.out.counts.set{res_counts}
       kb_marseq.out.report.set{res_report}
     break;